One frustration I had in the past with WordPress was organizing my link navigation. I tried for a while using the WordPress Navigation Tool (NAVT) plugin, but found that it was a bit quirky and unpredictable. Recently I’ve discovered and have been using the My Link Order plugin.
My Link Order allows you to set the order in which links and link categories will appear in the sidebar. Uses a drag and drop interface for ordering. Adds a widget with additional options for easy installation on widgetized themes.
This is one of my favorite WordPress plugins.